Yemen, with its key location in the Arabian Peninsula along a southern migration route out of Africa, represents a significant area of interest with respect to human migration. The prevalence of J haplogroups in the Arabian Peninsula and high frequency in European populations, suggests this group is ideal for understanding the European contribution and diffusion into the Arabian Peninsula and Africa. To facilitate the examination of genetic patterns in southern Arabia, Y-genotyping was employed to analyze 265 male samples, collected throughout Yemen. Specifically, 35% of samples were found to carry the J-12f2a-defining single nucleotide polymorphism, while 15% pertained to the DE-YAP-defined group, with the remaining 45% belonging to the F-M89 group. These J haplogroup samples were further genotyped to classify them into specific J haplotypes. After observing the resultant categories, the relative frequencies of each were compared with those of surrounding regions. Our results help illustrate the phylogeographic processes that shaped current genetic variation in Yemen with implications for a better understanding of the evolutionary history of the Arabian Peninsula.